conda-libmamba-solver
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conda
Solving environment... 3 days and still running...
Checklist
- [x] I added a descriptive title
- [x] I searched open reports and couldn't find a duplicate
What happened?
I installed miniconda3 and want to update my environment with the below packages. Is it normal to wait for >3 days for the resolution of the environment?
conda env update -f environment.yml
channels:
- bioconda
- conda-forge
dependencies:
- bamtools
- bamutil
- bbmap
- bcftools
- bedops
- bedtools
- bioblend
- biscuit
- bismark
- blast
- bowtie
- bowtie2
- bwa
- bwa-mem2
- bx-python
- cancerit-allelecount
- coreutils
- crossmap
- cutadapt
- cyvcf2
- deeptools
- deeptoolsintervals
- dnmtools
- dnaio
- dnapi
- ea-utils
- entrez-direct
- fadapa
- fastp
- fastqc
- fq
- galaxy-containers
- galaxy-tool-util
- galaxy-util
- gatk4
- geneimpacts
- gffread
- gffutils
- ghostscript
- gnuplot
- hisat2
- homer
- htslib
- ipython-cluster-helper
- jellyfish
- jemalloc
- jq
- k8
- kraken2
- libbigwig
- libgtextutils
- macs3
- methyldackel
- minimap2
- mirdeep2
- mirtop
- mosdepth
- msisensor-pro
- msisensor2
- multiqc
- munkres
- muscle
- ncbi-genome-download
- ncbi-vdb
- nextflow
- nf-core
- nf-test
- novoalign
- pblat
- perl-archive-tar
- perl-base
- perl-business-isbn
- perl-business-isbn-data
- perl-carp
- perl-common-sense
- perl-compress-raw-bzip2
- perl-compress-raw-zlib
- perl-constant
- perl-data-dumper
- perl-digest-hmac
- perl-digest-md5
- perl-encode
- perl-encode-locale
- perl-exporter
- perl-exporter-tiny
- perl-file-listing
- perl-file-spec
- perl-font-ttf
- perl-html-parser
- perl-html-tagset
- perl-http-cookies
- perl-http-daemon
- perl-http-date
- perl-http-message
- perl-http-negotiate
- perl-io-compress
- perl-io-html
- perl-io-socket-ssl
- perl-io-string
- perl-io-zlib
- perl-json
- perl-json-xs
- perl-libwww-perl
- perl-list-moreutils
- perl-list-moreutils-xs
- perl-lwp-mediatypes
- perl-lwp-simple
- perl-mime-base64
- perl-net-http
- perl-ntlm
- perl-parent
- perl-pathtools
- perl-pdf-api2
- perl-scalar-list-utils
- perl-socket
- perl-test-fatal
- perl-test-warnings
- perl-threaded
- perl-time-local
- perl-timedate
- perl-try-tiny
- perl-types-serialiser
- perl-url-encode
- perl-www-robotrules
- piper
- plink
- plink2
- popt
- picard
- preseq
- py2bit
- pybedtools
- pybigwig
- pyfaidx
- pysam
- pyvcf3
- qualimap
- randfold
- refgenconf
- refgenie
- rename
- rpsbproc
- sambamba
- samblaster
- samtools
- seqcluster
- seqkit
- snpeff
- snpsift
- salmon
- star
- stringtie
- subread
- tmb
- trim-galore
- trimmomatic
- ucsc-wigtobigwig
- umi_tools
- validators
- vcf2tsvpy
- vcftools
- viennarna
- weblogo
Conda Info
active environment : None
shell level : 0
user config file : /home/xxx/.condarc
populated config files : /opt/miniconda3/.condarc
/home/xxx/.condarc
conda version : 25.5.1
conda-build version : not installed
python version : 3.13.2.final.0
solver : libmamba (default)
virtual packages : __archspec=1=icelake
__conda=25.5.1=0
__cuda=12.2=0
__glibc=2.35=0
__linux=5.15.0=0
__unix=0=0
base environment : /opt/miniconda3 (writable)
conda av data dir : /opt/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/miniconda3/pkgs
/home/xxx/.conda/pkgs
envs directories : /opt/miniconda3/envs
/home/xxx/.conda/envs
platform : linux-64
user-agent : conda/25.5.1 requests/2.32.4 CPython/3.13.2 Linux/5.15.0-140-generic ubuntu/22.04.5 glibc/2.35 solver/libmamba conda-libmamba-solver/25.4.0 libmambapy/2.1.0 aau/0.7.1 c/. s/. e/.
UID:GID : 1000:1000
netrc file : None
offline mode : False
Conda Config
==> /opt/miniconda3/.condarc <==
channels:
- defaults
==> /home/xxx/.condarc <==
auto_activate_base: False
pinned_packages:
- conda>=25.*
- rsync>=3.3.*
- gatk4>=4.6.*
- libarchive>=3.7.*
- samtools>=1.18.*
- bcftools>=1.18.*
- numexpr>=2.10.2
- nf-core>=3.*
- transformers>=4.*
disallowed_packages:
- r-*
ssl_verify: /etc/ssl/certs/ca-certificates.crt
channel_priority: strict
channels:
- bioconda
- conda-forge
report_errors: True
Conda list
# packages in environment at /opt/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
_openmp_mutex 5.1 1_gnu defaults
anaconda-anon-usage 0.7.1 py313hfc0e8ea_100 defaults
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
archspec 0.2.5 pyhd8ed1ab_0 conda-forge
boltons 24.1.0 py313h06a4308_0 defaults
brotli-python 1.1.0 py313h46c70d0_3 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.19.1 h5eee18b_0 defaults
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
certifi 2025.4.26 py313h06a4308_0 defaults
cffi 1.17.1 py313h1fdaa30_1 defaults
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
conda 25.5.1 py313h78bf25f_0 conda-forge
conda-anaconda-telemetry 0.1.2 py313h06a4308_1 defaults
conda-anaconda-tos 0.2.0 py313h06a4308_0 defaults
conda-content-trust 0.2.0 py313h06a4308_1 defaults
conda-libmamba-solver 25.4.0 pyhd3eb1b0_0 defaults
conda-package-handling 2.4.0 pyh7900ff3_2 conda-forge
conda-package-streaming 0.11.0 pyhd8ed1ab_1 conda-forge
cpp-expected 1.1.0 hff21bea_1 conda-forge
cryptography 45.0.4 py313h6556f6e_0 conda-forge
distro 1.9.0 pyhd8ed1ab_1 conda-forge
expat 2.7.1 h6a678d5_0 defaults
fmt 11.1.4 h07f6e7f_1 conda-forge
frozendict 2.4.6 py313h536fd9c_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
jsonpatch 1.33 py313h06a4308_1 defaults
jsonpointer 3.0.0 py313h78bf25f_1 conda-forge
krb5 1.20.1 h143b758_1 defaults
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
libarchive 3.7.7 hfab0078_0 defaults
libcurl 8.12.1 hc9e6f67_0 defaults
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libgcc 15.1.0 h767d61c_2 conda-forge
libgcc-ng 15.1.0 h69a702a_2 conda-forge
libgomp 15.1.0 h767d61c_2 conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_2 conda-forge
libmamba 2.1.0 h430c389_0 conda-forge
libmambapy 2.1.0 py313hc41dfcf_0 conda-forge
libmpdec 4.0.0 h5eee18b_0 defaults
libnghttp2 1.57.0 h2d74bed_0 defaults
libsolv 0.7.30 he621ea3_1 defaults
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.1 h251f7ec_0 defaults
libstdcxx 15.1.0 h8f9b012_2 conda-forge
libstdcxx-ng 15.1.0 h4852527_2 conda-forge
libuuid 1.41.5 h5eee18b_0 defaults
libxml2 2.13.8 hfdd30dd_0 defaults
libzlib 1.2.13 h4ab18f5_6 conda-forge
lz4-c 1.9.4 h6a678d5_1 defaults
markdown-it-py 3.0.0 pyhd8ed1ab_1 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
menuinst 2.2.0 py313h06a4308_1 defaults
ncurses 6.5 h2d0b736_3 conda-forge
nlohmann_json 3.11.3 he02047a_1 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pcre2 10.42 hebb0a14_1 defaults
pip 25.1.1 pyh145f28c_0 conda-forge
platformdirs 4.3.8 pyhe01879c_0 conda-forge
pluggy 1.6.0 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py313h5eee18b_2 defaults
pycparser 2.22 pyh29332c3_1 conda-forge
pydantic 2.11.4 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.2 py313h4b2b08d_0 conda-forge
pygments 2.19.1 py313h06a4308_0 defaults
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.13.2 hf623796_100_cp313 defaults
python_abi 3.13 7_cp313 conda-forge
readline 8.2 h8c095d6_2 conda-forge
reproc 14.2.5.post0 hb9d3cd8_0 conda-forge
reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge
requests 2.32.4 pyhd8ed1ab_0 conda-forge
rich 14.0.0 pyh29332c3_0 conda-forge
ruamel.yaml 0.18.14 py313h536fd9c_0 conda-forge
ruamel.yaml.clib 0.2.12 py313h5eee18b_0 defaults
setuptools 80.9.0 pyhff2d567_0 conda-forge
simdjson 3.12.3 h84d6215_0 conda-forge
spdlog 1.15.3 h10b92b3_0 conda-forge
sqlite 3.46.0 h6d4b2fc_0 conda-forge
tk 8.6.14 h39e8969_0 defaults
tqdm 4.67.1 py313h7040dfc_0 defaults
truststore 0.10.1 pyh29332c3_0 conda-forge
typing-extensions 4.14.0 h32cad80_0 conda-forge
typing-inspection 0.4.1 pyhd8ed1ab_0 conda-forge
typing_extensions 4.14.0 pyhe01879c_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 2.3.0 py313h06a4308_0 defaults
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xz 5.8.1 hbcc6ac9_2 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge
xz-tools 5.8.1 hb9d3cd8_2 conda-forge
yaml-cpp 0.8.0 h6a678d5_1 defaults
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.23.0 py313h536fd9c_2 conda-forge
zstd 1.5.6 hc292b87_0 defaults
Additional Context
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